Prime Minister Tony Abbott has played down the impact of the International Court of Justice's whaling decision on Australia-Japan relations, saying the relationship between the two countries, was "much, much, much" bigger than the disagreement.

Speaking to reporters in Perth on Tuesday afternoon, Mr Abbott said that it was up to Japan to "reflect" on the court's ruling that Japan’s whaling program was not for scientific research and should stop.

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"I'm sure that’s exactly what will happen," he said. "Japan is an exemplary international citizen."

Mr Abbott is due to fly out to Japan on Saturday for his first visit to the country as Prime Minister, where he will try and finalise a free trade agreement with Australia's second-largest trading partner.

He dismissed any suggestion that the ICJ decision would hamper relations between the two countries, even though the court had agreed with Australia's long-held view that Japan’s JARPA II research program was not for the "purposes of scientific research".

Mr Abbott said he was looking forward to his trip and noted that the bilateral relationship was "certainly much, much, much bigger than any disagreement we might have had about whaling," he said.

Also on Tuesday, opposition leader Bill Shorten described the ICJ ruling as a vindication of Labor’s decision to take the original court action. The Rudd government sought an order from the ICJ to stop the Japanese whale hunt in 2010, and Mr Shorten said that had ultimately led to a decision that would be welcomed by most.

"This is great news for everyone who wants to see whales protected and not hunted for commerce," Mr Shorten said.

"The decision that Labor made to take this to the international court was a policy that was not supported by [Prime Minister] Tony Abbott.

"The wisdom of the approach was vindicated by this successful decision. Our seas will be better for it."

On Tuesday, Mr Abbott said he appreciated "the desire of the Australian people generally to see an end to whaling in the Southern Ocean".

"That's certainly been an objective of both sides of politics for a long time."

Mr Shorten also said he did not think the decision would affect Australian-Japanese relations.

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Prime Minister Tony Abbott remains hopeful that delicately poised Free Trade Agreement negotiations with Tokyo will not be derailed by Australia's win in the International Court of Justice against ''scientific'' whaling.

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When the world's last whaling factory ship ,the Nisshin Maru, left the Antarctic at the end of this past summer, it did something different. For most of its existence, Japan's ''research mother ship'' has been harassed in the far south by anti-whaling activists who have made it their key target. Consequently, its movements have usually been shrouded in secrecy.

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Maritime environmental activist group Sea Shepherd has claimed victory for the ending of Japanese whaling in the Southern Ocean following a United Nations ruling that the program was not scientific.